5. ChimeraX Operate protocol

Protocol designed to perform operations with atomic structures in Scipion by using ChimeraX. A volume or set of volumes can also be included. Structures or maps generated by using this protocol can be saved in Scipion after executing specific ChimeraX commands. ChimeraX rigid fit protocol constitutes a particular case of this protocol to perform rigid fitting in Scipion by using ChimeraX (Appendix CHIMERA Rigid fit).

• Requirements to run this protocol and visualize results:
  • Scipion plugin: scipion-em
  • Scipion plugin: scipion-em-chimera
• Scipion menu: Model building -> Tools-Calculators (Fig. 5.2 (A))
  

  Fig. 5.2 Protocol chimerax-operate. A: Protocol location in Scipion menu. B: Protocol form.

• Protocol form parameters (Fig. 5.2 (B)):
  • Input section
    • Input Volume: Optional parameter to be completed with the electron density map previously downloaded or generated in Scipion.
    • Input additional Volumes: Optional parameter to include other electron density maps previously downloaded or generated in Scipion.
    • Atomic structure: Atomic structure previously downloaded or generated in Scipion.
    • Other atomic structures: Additional atomic structures.
  • Help section
    This section contains ChimeraX commands required to save models according to their reference volumes, which can also be saved if required. Remark that using scipionwrite command, ChimeraX session will be saved by default, without prejudice that it may be saved with scipionss command. scipioncombine command allows to merge in only one atomic structure two or more structures. ChimeraX sessions can be restored by using chimerax-restore session protocol.
• Protocol execution:
  Adding specific protocol label is recommended in Run name section, at the form top. To add the label, open the protocol form, press the pencil symbol at the right side of Run name box, complete the label in the new opened window, press OK and, finally, close the protocol. This label will be shown in the output summary content (see below). If you want to run again this protocol, do not forget to set to Restart the Run mode.
  Press the Execute red button at the form bottom.
  ChimeraX graphics window will be opened after executing the protocol. Electron density map(s), if loaded, and the atomic structure(s) are shown. Steps to follow depend on the specific operation to carry out. Usually, new volumes or structures are generated, sometimes by combination of others, each one with a specific model number displayed in the Models panel, and they have to be saved in Scipion.
  • To combine two or more atomic structures, write in ChimeraX command line:

    scipioncombine #n1,n2
    

    #n1 and #n2 are the respective model numbers of two different atomic structures. Optionally you can set the model number of the output combined structure #n3:

    scipioncombine #n1,n2 modelid n3
    

  • To save a map or an atomic structure generated with this protocol model number #n, write in ChimeraX command line:

    scipionwrite #n
    

    Optionally you can write a prefix to easily recognize that map or structure. Then, the prefix depends on the user. Example:

    scipionwrite #n prefix my_favorite_model_
    

  • Close ChimeraX graphics window.

• Visualization of protocol results:

  After executing the protocol, press Analyze Results and Chimera graphics window will be opened by default. Atomic structures and volumes are referred to the origin of coordinates in ChimeraX. To show the relative position of atomic structures and electron density volumes, the three coordinate axes are represented; X axis (red), Y axis (yellow), and Z axis (blue) (Fig. 5.3). Coordinate axes, volume, and atomic structure are model numbers #1, #2, and #3, respectively, in ChimeraX Models panel. If no volumes have been included, coordinate axes and each atomic structure are model numbers #1 and #2, respectively.

  

  Fig. 5.3 Default ChimeraX graphics window with coordinate axes.

• Summary content:

  • If an atomic structure is generated:

    • Protocol output (below Scipion framework):

      chimerax - operate -> output atomic structure name, starting with the prefix;

      AtomStruct (pseudoatoms=True/ False, volume=True/ False).

      Pseudoatoms is set to True when the structure is made of pseudoatoms instead of atoms. Volume is set to True when an electron density map is associated to the atomic structure.
    • SUMMARY box:

      Produced files:

      output atomic structure name, starting with the prefix (.cif file)

      we have some result

  • If a volume is generated:

    • Protocol output (below Scipion framework):

      chimerax - operate -> output 3D map name; Volume (x, y, and z dimensions, sampling rate).
    • SUMMARY box:

      Produced files:

      output 3D map name, starting with the prefix (.mrc file)

      we have some result